Regarding my second question, I have been experimenting with the cosine content using different portions of the trajectory and these are the results I got for the first principal component:
proj-ev1_coscont_0-5ns.xvg 0.0174761 proj-ev1_coscont_0-10ns.xvg 0.0283423 proj-ev1_coscont_0-15ns.xvg 4.16906e-06 proj-ev1_coscont_0-20ns.xvg 0.0689592 proj-ev1_coscont_0-25ns.xvg 0.161691 proj-ev1_coscont_0-30ns.xvg 0.298431 proj-ev1_coscont_0-35ns.xvg 0.535732 proj-ev1_coscont_0-40ns.xvg 0.767029 proj-ev1_coscont_0-45ns.xvg 0.885829 proj-ev1_coscont_0-50ns.xvg 0.906473 proj-ev1_coscont_5-50ns.xvg 0.8823 proj-ev1_coscont_10-50ns.xvg 0.751018 proj-ev1_coscont_15-50ns.xvg 0.537473 proj-ev1_coscont_20-50ns.xvg 0.357136 proj-ev1_coscont_25-50ns.xvg 0.145889 proj-ev1_coscont_30-50ns.xvg 0.0150995 proj-ev1_coscont_35-50ns.xvg 0.00123905 proj-ev1_coscont_40-50ns.xvg 0.00675679 proj-ev1_coscont_45-50ns.xvg 0.0105643 The total time I have run the simulation was 70ns, but judging from the steep increase of the RMSD (RMSD plot attached), I decided to exclude the first 20ns from the analysis. Hence the cosine content values above correspond to the last 50ns and the counting starts from the 20th ns. Clearly the convergence of the last 50ns is not good (proj-ev1_coscont_0-50ns.xvg: 0.906473), but the PC1 plot (attached) shows a steep decrease at ~30ns which looks like a conformational transition. It is also evident that the cosine content decreases drastically approximately at that point (25-50ns: 0.145889, 30-50ns.xvg: 0.0150995, 35-50ns.xvg: 0.00123905, etc.) and reached values that are not bad. Unfortunately, extending the simulation is not an option due to lack of time (I am forced to finish the manuscript soon). So would you recommend doing essential dynamics for the last 20ns? I would GREATLY appreciate any comments!!! Thomas On 7 March 2012 21:56, Thomas Evangelidis <teva...@gmail.com> wrote: > > Dear GROMACS community, > > I have two questions regarding PCA. I have run MD simulations for 70 ns > for a protein of 1100 amino acids, of which I decided - based on the RMSD - > to analyze the last 50. > > 1) The protein consists of 5 domains, out of which only one is of interest > in this study. Is it right to do draw conclusion from PCA restricted that > domain (400 aa)? > > 2) How can I find out if the simulation time is sufficient to do PCA? > > Thanks in advance for any feedback. > > Thomas > > >
<<attachment: proj-ev1.png>>
<<attachment: totalWT+C2_70ns_protein_caRMSDvsTIME.png>>
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